Sugo is called into a meeting with the two flight teams. General Monto Minatoya, Colonel Yoshito Takaesu and his bodyguard, Tomonaga. They inform the teams about a mission to an area of hostilities known as the Southeast Asian Union (SEAUn). The mission is part of Japan's assistance to SEAUn government against rebel forces. It is called Operation Foot Stamp. Sugo's unit is tasked to provide support to SEAUn assault on a major rebel base. Sugo and Sarutobi take off and eventually enter the area of active warfare. Sarutobi starts the cover mission for SEAUn ground forces led by Otomo's squad. But Sarutobi's drone is hit by ground fire and Sugo who tries to continue the mission is out of ammo. Sugo is ordered to retreat after dropping what he believes to be emergency supplies for Otomo's squad. Unfortunately, the squad is lost and listed as Missing in Action (MIA), although it's assumed they are all dead, including Otomo. When Sugo visits Rin and tells her what happened, she slaps him. Sugo's hue begins to cloud with guilt and Rin leaves the military, after which she miscarries her unborn child.
Three months later, an unmanned drone attacks the Ministry of Defense building, killing many government officials and wounding others, including Takesu. Inspector Risa Aoyanagi and Enforcer Tomomi Masaoka arrive on base to look for the culprit, who they determine must be someone capable of operating such sophisticated craft. They meet Sugo in Minatoya's office where Masaoka shows him a recent image of a figure inside a drone; it is Otomo. Sugo defends his friend and Minatoya says that even if Otomo is guilty, he is untouchable as military personnel. Aoyanagi says that Otomo is now a civilian and can be arrested. It is then revealed that the terminal used to control the attack drone belonged to Sugo, who is now a primary Person of Interest. Aoyanagi and Masaoka begin to follow Sugo and question his actions. Masaoka suggests they work together to find Otomo and clear Sugo of suspicion.
Skip to a moving automobile with Inspector Nobuchika Ginoza, Enforcer Shinya Kogami and Enforcer Shusei Kagari on their way to Dejima (Kyushu region). Meanwhile, Aoyanagi, Masaoka and Sugo visit Rin, who says she's certain Otomo would get in touch with her if he were alive. Masaoka probes her many leaves of absence from her new job, but Rin replies she just needs rest and medication to feel better, without mentioning her clouded hue. Still, Masaoka's suspicions are raised, though he now believes Sugo is innocent.
As the trio drives back to the city, Aoyanagi mentions that they're in a "certain neighborhood" and brings Masaoka to visit his ex-wife, Sae, an invalid suffering from Eustress Deficiency, but allowed to live at home with a nursing bot. While they wait in the car, Sugo asks Aoyanagi about Masaoka. Aoyanagi praises the former detective whose diligence during horrific cases caused his crime coefficient to rise and eventually made him a latent criminal simply for doing his job.
Now in Dejima, Ginoza makes contact with Aoyanagi's team. He says that Otomo has been seen in the area, then chastises Masaoka after learning about his visit to Sae. During his second contact with them, another drone attacks the Ministry of Foreign Affairs building and many are killed, including Kyokei Fukita, a Ministry counselor Sugo recognizes. He mutters, "Foot Stomp," but doesn't elaborate. Masaoka hears this and asks Analyst Shion Karanomori to check things out. Meanwhile, Ginoza, Kogami and Kagari search Sugo's hotel residence without finding any evidence.
Sugo alone meets with Minatoya who attempts to put him off the track, then arrests and begins to torture him, only to be stopped by Aoyanagi and Masaoka. They inform Minatoya that the crime coefficients of those on the base aren't good and that they suspect the military of being complicit in the bombings. Minatoya menaces Masaoka with statements about Sae and Ginoza's welfare, to which Masaoka warns the general about his latent criminal status and its unspoken threat.
Away from Minatoya, Masaoka tells a rescued Sugo that he has several safe houses should Sugo need one. He also wonders aloud if Otomo had any kind of "insurance" like that. That's when Sugo remembers his friend's past words about a bottle of brandy being "insurance" and brings it to the team. When they find a hidden chip hidden in the brandy bottle's cap, they view its contents. Seeing images of a moored nuclear submarine among other data, the team heads to where the abandoned vessel is located underground in an unused port that is a part of a former U.S. base in Dejima.
Outside, Otomo is spotted by Ginoza's team and they give chase. When Kogami catches up to the man, they struggle, both falling through an open air shaft. Although he cushions Kogami upon landing, Otomo gets up unharmed and flees. Lights come on in the mooring and Aoyanagi's team sees the sub. Otomo arrives in the same area and struggles with Aoyanagi until he pushes her and she falls, rolling into the water. Masaoka jumps in to rescue her. Sugo catches up with Otomo and they also fight until Sugo subdues Otomo, who turns out to be a sparring bot. Kogami arrives and the group watches as the bot shares its secrets about Operation Foot Stomp and the truth about what happened to the ground troops. When Sugo learns that he dropped poisonous gas instead of emergency supplies, killing his squad and Otomo, he is devastated. The bot then reveals Rin's complicity in setting up the Otomo-bot as a decoy so she could exact revenge for being forced back into the military, her miscarriage and the death of her husband.
Sugo rushes back to base only to find Minatoya has been murdered by Rin, now dressed in guerilla clothing. When Sugo tries to stop her rampage, she turns and shoots Takaesu at his desk, killing him as well, only to discover that he is Tomonaga using a Takaesu-holo disguise. The real Takaesu enters the room and shoots her. Sugo cradles Rin's dead body, another friend lost and his hue further clouding. Later, off base, the real Takaesu is confronted by Aoyanagi, Masaoka and police bots. When he tries to escape, Masaoka's Dominator reads his crime coefficient at 340 and the Sibyl System gives the order to use Lethal Eliminator on him. Takaesu is destroyed.
At the same spot where the flight team once socialized, Masaoka and Sugo meet up. Otomo and Rin are deceased, along with the ground troops, Minatoya, Takaeku, Tomonaga and Fujita. Sugo is no longer able to continue in the military because of his greatly clouded hue. Masaoka urges therapy, then suggests that he do police work, like himself. Sugo eventually becomes an Enforcer in Division 01, having been labeled a latent criminal. Hanashiro is again seen asking him to join her teams. He refuses, his willingness to remain an Enforcer his way of honoring the now-deceased Masaoka.
Hanashiro says she will keep trying.